A Different Kind of Homecoming
by blueEyes206
Summary: Returning to a familiar yet foreign world is never easy, especially after nearly four years.
1. The Return

**A/N: I'm new to this whole fanfic thing... I don't know if this will be any good, and it's probably a used concept, but this idea (among others) wouldn't leave me alone, and this one seemed to write itself so easily, so I went with it. **

Seeley Booth took a deep breath as he walked up the stairs of the apartment building. He had climbed these stairs many times before, but the last time had been nearly four years ago. A new color of paint had been applied to the walls, and he thought it looked nice. He shakily exhaled the breath he didn't know he'd been holding and approached the door of the apartment to which he was headed. He stood quite a few feet away from it, staring and thinking.

He was tired. He looked like crap. His pain was so excruciating he didn't know how he had made it up the stairs. He knew he should have stayed in the hospital for longer, but he couldn't stand it any longer. It had been almost four years since he'd seen her. Four torturous years, not just emotionally, but physically as well. Would she be as mad as she had been when he had "died" and didn't tell her? Hopefully not, as this time hadn't been his fault. _But you could have stayed. You didn't have to go_, a voice inside his head whispered. _What about duty and honor?_ another voice countered. Great, now he felt as if he were in a cartoon with a devil Booth on one shoulder and an angel Booth on the other.

Booth was shaking. Suddenly, noises from inside the apartment shook him from his jumbled thoughts. Cheerful noises. Noises of laughter and squeals. The laughter and squeals of young children. Confusion washed over him. Had she moved? It was possible; it _had_ been nearly four years. But then he heard an adult voice. _HER_ voice. A voice which he thought he might never hear again. His brain didn't register what she had said, it was too focused on the wonderful, beautiful sound.

Curiosity had gotten the best of him and helped him to overcome his fears. He moved closer to stand directly in front of the door, but did not knock. He listened carefully, trying to determine why children's voices were echoing in her apartment. He racked his brain, trying to think of an explanation. Her nieces, Hayley and Emma? But no, it had been nearly four years. They had grown, just as his own son had grown, without him there to witness it. Then her voice interrupted his thoughts again.

"Okay, girls, put the movie in, and you can watch a little bit before bed."

_Put the movie in? Where? Bones didn't own a TV, _Booth thought to himself. _And since when does she sound so gently and motherly? Not that she was incapable..._

"Tempe, how big is your TV again?" a little voice piped up.

"103 inches."

No way. She had a TV of the same proportions that he had mentioned all those years ago? It was impossible. Booth had never been more confused, except for maybe when he had woken up from his coma, thinking Bones was his wife. That had been pretty darn confusing.

Suddenly, Booth began to chicken out. He backed away from the door and turned to go down the stairs. He had made it halfway down when he slumped to the floor against the wall. Tears welled up in his eyes. God, he missed her so much. The sound of her voice was intoxicating. All he could think about was the last two weeks he had spent with her. The nights of passion, the mornings of passion. She had even taken off time from work to spend it with him. Feelings had been declared, lines had been obliterated, love had been made, and they'd never been more happy. But then he'd left her, just like everyone else in her life. Why would she let him back in now? He had betrayed her trust, even though he said he wouldn't.

But her voice - it had sounded happy and satisfied. His curiosity piqued again, and he pushed himself off the floor and traveled up the stairs, determined to actually knock this time. This time as he approached the door, he heard more laughter and distinct lines of the movie which was playing.

"Hey, Mr. Grumpy Gills. When life gets ya down, ya know what ya gotta go? Just keep swimming, just keep swimming, just keep swimming, swimming, swimming. What do we do? We swim, swim, swim."

Booth instantly recognized the lines. Parker had loved that movie. But what was it doing playing in Bones' apartment? She was seriously watching a cartoon movie about talking sea creatures? Then he heard another strange sound he hadn't noticed before - the giggle of an infant. Now he _had_ to know what was going on!

He shakily took a deep breath as he raised his hand to knock on the door. _It's now or never, Seels. You're not a coward, and you love this woman. So man up!_ he told himself.

Booth softly knocked at the door. His heart was beating rapidly, so rapidly he thought it might explode. Despite the throbbing of his heart which he could hear in his ears, he heard the lock click, and then the apartment door opened slightly.

There she was. All five feet nine inches, one hundred some pounds of her. She was almost four years older, but it didn't show at all. In fact, she looked even younger, if that was possible. Her beauty was incredibly breathtaking. She was dressed comfortably - a light grey wife beater tank top paired with black sweatpants reading NORTHWESTERN in royal purple down her right leg. Instead of her usual larger jewelry, her necklace was a simple silver dolphin, and her earrings were square diamond studs. Her hair was different, back to a brownish color, which he suspected was closest to her natural color, but the auburn and blonde in it still shone slightly in the light. It was rather long and pulled back loosely into a braid at the nape of her neck, and she had long side swept bangs which covered the corner of her right eye. Her eyes - those gorgeous, expressive, grey-blue eyes - were still the same; at first, he detected a genuine smile behind them, but as she realized who was standing in front of her, those expressive eyes reflected shock and - was that fear? But perhaps the most shocking thing of all was the small blond-haired infant who gurgled as she bounced him in her arms.

"Booth."


	2. The Shock

"Booth." Her voice came out in a whisper barely loud enough for him to hear.

"Bones," he spoke quietly, tears forming in his eyes yet again.

Her mouth opened and closed for a few seconds, and he thought he saw her blink tears out of her eyes before she turned around to face the three young girls in her apartment.

"Girls," she began, trying to calm her raging emotions, "can you take the movie out and watch it on the laptop in your room? You can go ahead and finish the movie if you like. I need to talk to someone out here alone."

"Okay!" the three girls shrugged and skipped out of sight to their bedroom.

Brennan took a deep breath and turned back around to face Booth. She was shaking and feared that it was visible to the man standing in front of her - the man she loved. She was no longer afraid to admit that. She had admitted it to him before he left and told him each time she had talked to him during the first few weeks, but then he had disappeared. At first Brennan thought that he had left her, like everyone else had. But then she realized that Booth would never have done that to her. Once this realization had set in, she began to worry. There was no evidence that he was dead, but he certainly couldn't be fine; he would have called if he had been fine.

That nearly four-year period was challenging for her - a time of monumental changes in her life, and at first she had been scared to death of dealing with it all without Booth. As much as she didn't want to rely on another for support, she knew she needed him. He was her rock, the one who always understood her and accepted her and helped her when she needed it. In the end, it had been the thought of what Booth would do that kept her going through it all. Somewhere deep inside her, Brennan had a glimmer of hope that he would return to her, but she steeled herself for the more distinct possibility of never seeing him again.

And now, here he was, in the flesh and not just her dreams or a picture, standing in the doorway of her apartment. She studied him carefully. He was thin - too thin, she noticed; he had lost an unhealthy amount of weight. Bruises, cuts, scars, and stitches covered his handsome face, and his normally warm and reassuring chocolate brown eyes were sunken and filled with tears. His posture was slumped, and he looked worn and beaten. He was carrying himself as if he had several broken ribs, and a rather large bandage appeared on his right forearm.

"Oh, Booth," she whispered quietly, shifting the infant's weight to her left hip and reaching out to touch his face with her right hand. She caressed the side of his face and left her hand there, lightly tracing one of his deeper cuts with her thumb. Quiet tears began to run down both of their cheeks as Booth raised his left hand to cover hers. He gently rubbed her hand, relishing the relief she brought him. This relief was equal parts relief at seeing her and feeling her again as well as relief that she hadn't begun to love another in his place.

"Bones, oh, baby, I've missed you so much," he declared, tears now flowing freely down his face, stinging the still raw cuts all over his face.

Brennan didn't respond, only leaned in to kiss his lips gently. He began to wrap his arms around her to deepen the kiss, but the baby in her arms squirmed and began to whimper, causing her to reluctantly pull back from the embrace.

"We're squishing Liam, and it's his bedtime anyway," she said, turning her back to Booth and walking into her apartment. Getting as far as the hallway, she sensed that Booth was still standing in the doorway. She paused and turned. "You can come in, you know, Booth. I apologize if it's a bit messier than you're used to."

"Maybe... maybe I should just go, Bones. I don't want to be in your way here or anything," he said nervously.

"Don't worry about it. Just make yourself comfortable, and I'll be right back as soon as he falls asleep."

Brennan gave him a soft half-smile before turning to walk toward what Booth knew was her bedroom. She was keeping the baby in her own bedroom? Booth's head was spinning. He took a look around her apartment, which was almost completely different from the last time he had seen it.

For one thing, it had been child-proofed. Most of her bookshelves and furniture were still there, but all of the electrical outlets close to the ground had been plugged, and every artifact she had collected was missing, or placed near the ceiling. Children's toys, mostly those that girls would enjoy, were everywhere. Her refrigerator was covered with alphabet magnets and children's drawings.

As he looked into her living room, he saw the television mounted in all 103 inches of its glory. He shook his head at the sight of Bones having a television, much less one that large. What was even more strange was the collection of movies stored beneath the TV. He perused the titles: _Cinderella, Sleeping Beauty, Snow White and the Seven Dwarves, Finding Nemo, Madagascar, 101 Dalmatians... _The list of Disney movies and other various cartoons continued. Of course there were a few movies that were more age-appropriate for Bones herself, but the majority were children's films.

Feeling light-headed from the confusion he was experiencing, Booth collapsed onto her couch. Then he noticed the picture frames. How could he have missed them? They were all over her apartment. Steadying himself, he began to look at all of them. Most of the pictures were of two small girls who appeared to be twins, both with brown hair and one with grey-blue eyes and one with chocolate brown eyes. There were pictures of the girls at the lab in Bones' office, pictures of them at a pond with a tennis court in the background (_Must be Hodgins' place,_ he thought to himself), pictures of Bones laughing while playing with the two, a picture of Bones looking exhausted and holding two newborn infants. Were these _her_ twin daughters? But who was the other older girl? And who was the baby? There were no pictures of them in her apartment.

It was the final picture he saw that threw him for a loop - a boy with long, curly, dark blond hair who looked to be about eleven standing between the two twins with his arms around them. The boy was wearing what Booth referred to as a "Junior Squint lab coat," and despite how long it had been, Booth knew who the boy was. He squinted closely at the picture to confirm his hunch - in tiny cursive on the left breast of the coat read "P. Booth."

Booth stumbled back the couch and sat down. Was he in another coma, having another weird dream? _What_ was going on here?


	3. His Story

**A/N: Thanks for reviewing so far! This chapter seems a bit longer, but it really isn't that much longer than the others. **

Booth sat on the couch, his head in his hands, rubbing his temples with his fingers. He felt so guilty for being gone for such a long period of time. His inner Bones told him that his guilt was irrational, for he could not have prevented everything that had happened to him. But no matter how hard he tried, he still felt like he had abandoned his son and worst of all, abandoned Bones, who had already been abandoned enough in her lifetime.

That guilt, combined with the extreme confusion of what was going on in Bones' life, was making him feel dizzy and nauseous. He lay down on the couch, trying to relieve his pain. He shut his eyes for a brief moment, and the next thing he knew, he heard a door softly clicking shut. He jerked awake at the sound and abruptly sat up. He didn't want Bones to come in and find him crashing on her couch; he desperately wanted to talk to her.

But Bones didn't come back to the living room immediately. Booth could see her walk across the hall and open the door into what he knew as her guest room, but now he assumed it was the room that those three little girls shared. He shook his head for what seemed to be the millionth time in the last hour or so. Bones had three little girls and a baby boy living in her apartment. He just couldn't get used to the idea.

As Brennan backed out of her bedroom after putting Liam to bed, she saw Booth asleep on her couch. She tried to move quietly, but when the door clicked shut, Booth bolted into a sitting position. He seemed awfully jumpy, and she couldn't imagine why. He knew that he could be at home here. Brennan wasn't very good at reading people - not good at all, really - but she could always read Booth. This time, however, was different. She couldn't tell why he was acting the way he was. Granted, this situation was a bit awkward, since so much time had passed. But still, something was bothering him, and it wasn't obvious. _What happened to him?_ she wondered.

She walked into the girls' room to find all three asleep in the bottom bunk of the bunk, snuggled close to one another, and the movie still playing on her laptop at the foot of the bed. Deciding that they looked comfortable and peaceful, she simply stopped the movie and covered the three sleeping angels with a blanket. She sighed, thinking that one of Booth's problems could certainly be confusion at seeing her interact with such small children. She'd never really had any "people skills," and she was generally awkward with children, never knowing exactly what to say to them. She pursed her lips as she often did when she was nervous, wondering how she was going to explain everything to Booth.

Booth was sitting on the couch staring at his shoes when he heard Brennan's soft footsteps entering the room.

"Are your shoes really that interesting, Booth?" she asked softly as she approached him.

He looked up, somewhat embarrassed. After all, he felt like he had been snooping around her apartment by looking at her pictures.

"Uh, no, not really. I just spaced out, that's all."

A puzzled look appeared on her face, and Booth couldn't help but smile. _Ahh, some things never change,_ he thought appreciatively.

"It's an expression, Bones. Means that I was staring at my shoes, and I didn't really know that I was doing it."

"Oh," she said even more quietly, as she placed her laptop on the coffee table and sat next to him on the couch.

They looked into each other's eyes for a moment, grey-blue meeting chocolate brown in a soft, yet intense gaze. After a while, Brennan blinked and turned her head forward, breaking the impromptu staring contest. She took a deep breath and faced him again.

"I missed you," she stated, in a very matter-of-fact manner, trying to hold back tears.

"I missed you, too, Bones. You have no idea how much..." Booth's voice broke on the last word, and he struggled to keep from crying in front of her. _Toughen up, Booth. You're a soldier. Don't let her see you cry!_ he thought.

"Hey, hey..." she whispered, running her fingers through his hair. "Shhh, Booth. It's okay. I'm right here."

He wrapped his arms around her and pulled her close, ignoring the excruciating pain that rippled through his chest and abdomen from his broken ribs. He just needed to hold her. Brennan, with all her genius, however, could tell that he was in pain and gently pulled back from the embrace.

"Booth, what happened to you?" She looked over his thinner frame with concern. Booth stifled a laugh at her bluntness. At least she'd been a little bit tender before jumping straight to the core of things.

"Nothing that can't be fixed, Bones. No big deal," he said, trying to change the subject. But she wasn't having any of it.

"Booth, you have several broken ribs, stitches on your face, a bandage on your arm, you've lost too much weight, bruises covering your body, and those are only the things I can see!" she was becoming visibly upset. "You should be in a hospital, not here."

"I was, Bones. After a week of being poked and prodded, I'd had enough. I could move at least a little better than I could when they found me, and I couldn't take it anymore. I needed to see you. I made them release me."

"Found you where?" she questioned quietly.

Booth knew she would have picked up on that and regretted saying anything. Why couldn't she have picked up on the fact that he left the hospital in order to come back to her?

"Booth, just tell me what happened. You were undercover, obviously, and something went terribly wrong." She knew she was being blunt and genuinely felt badly about it, but he wouldn't respond to her any other way.

Booth hesitated. He knew she wouldn't stop pressing for details, so he had to tell her. He took her hand, rubbing circles with his thumb on her soft, fair skin.

"The guys we were trying to catch, they, uh, they found our safe house and stormed it. Killed all of the men except me and one other agent. Why the two of us? I don't know, but they dragged us to their hideout and tortured us for information. Once they realized we weren't going to give up any information, they killed the other agent right in front of me." Brennan felt Booth shiver at this point of his story, and she brought his hand up to her lips and kissed it softly.

"It's okay, Booth. You don't have to go on if you don't want to," she reassured him, tears welling in her own eyes.

"There's not much more to tell. For the next... three years, I guess, they kept me alive, somehow figuring it was more fun to torture me than to kill me. Every time they thought the FBI was catching on to their location, they moved to a new one. About a week ago local FBI finally found us, killed all of the terrorists, and shipped me off to a local hospital. I had to catch a plane from Seattle to get here."

"Oh, Booth," Brennan found herself saying for the second time that night. She wondered when she had become so speechless. Probably around the time he first said 'I love you,' she guessed, even that ridiculous qualifier had been added.

She leaned in to kiss him, and he met her halfway. The kiss started out soft and slow, but soon became filled with longing and passion. Not caring how much pain it would cause him, Booth leaned so that he was practically lying on top of her on the couch. It had been far too long since he'd been close to her. She pushed his t-shirt up to run her hands over her back and found that his back was covered with cuts and scars as well. A mixture of relief and anger washed over her - relief that he was still alive and anger that he had been tortured yet again. This sensation made her more passionate, and her kisses became deeper and more intense.

Suddenly, a high-pitched shriek followed by hysterical crying came from the girls' bedroom.


	4. Her Story

**A/N: Thanks, you guys, for all of your lovely reviews! They're much appreciated! Here's the next chapter... I don't know, something about this one didn't feel right to me, but I didn't know what else to do with it. I think it's the girls' dialog. I SUCK at writing for kids (even though I myself babysit a three-year-old!). **

At the sound of the shriek, Booth bolted off the couch and started for the bedroom.

"Booth, wait," Brennan said calmly. "Let me handle this." She walked quickly but calmly to the girls' room and opened the door slowly.

Booth's heart was beating rapidly. What was going on here? Bones seemed so calm, not in the slightest bit frantic. Did this happen often? Who had screamed? And why? He hated feeling useless and in the dark.

Brennan walked into the girls' room to find all three girls crying, but six-year-old Lydia crying the hardest.

"Hey, hey, sweetheart, what's wrong?" she asked gently, sitting on the edge of the bed.

The little girl shook her head violently, sending blonde curls flying. Brennan wrapped her arms around Lydia and pulled the girl into her lap. Lydia buried her head in Brennan's shoulder, still crying hysterically.

While rubbing Lydia's back, Brennan turned her attention to the twins, whose crying had quieted significantly. The brown-eyed twin had scooted herself all the way against the wall, and her face was twisted into an uncomfortable expression, while the grey-blue-eyed twin stared at the ground, seeming ashamed. It was the brown-eyed twin that spoke first.

"Lydia woke up screaming, and Ellie wet the bed," she stated bluntly

Brennan looked sympathetically at little Ellie, who sniffled before nodding her head to confirm her sister's story. Without letting go of the crying girl in her lap, Brennan reached out to ruffle the hair of the distraught three-year-old.

"It's okay, honey. It just startled you. Why don't you girls get a new pair of pajamas and go to the bathroom and clean up, okay? I'll be there in just a minute."

The twins nodded, gathered new clothes, and walked out of the room. Brennan refocused on Lydia, who had started hiccuping from crying so hard. "What happened, Lyd?" Brennan asked, stroking the girl's soft curls. "The nightmare again?"

Lydia pulled back and looked at Brennan, eyes still filled with tears. "It was the man, he came and tried to kill you and Ellie and Evie this time, and I was all alone with Liam again..." She burst into tears again. "I really miss Mommy and Daddy..."

"Shh, okay, it's alright, you're okay. I'm right here. I'm not going anywhere," Brennan reassured her. "Do you want me to get you a glass of water for your hiccups?"

Lydia nodded, and Brennan began to let go of her, but Lydia only tightened her grip around Brennan's neck.

"No! Don't leave me!"

"Okay, honey, just let me go check on the girls, and then we'll get some water."  
Brennan hoisted the girl onto her hip, and after checking on Ellie and Evie, who were now taking a bath.

As Brennan entered the living room to cross into the kitchen, Booth opened his mouth to ask what was going on, but she silence him with a slight shake of her head. Brennan opened her cabinet and got down a small glass and filled it with cold tap water.

"Here, sweetie, drink this."

Booth was amazed, and he felt his heart swell with pride at seeing his Bones interact with this upset little girl so lovingly. Even though he had no idea who the little girl was, it was clear to him that Bones loved her. She had changed so much while he was gone; she was wearing her emotions on her sleeve now, and he wondered what exactly she had gone through to get to this point. A small, worried voice broke up his train of thought, however, sending him into a panic.

"Tempe, why is there a man in your living room?"

Booth looked at Brennan apologetically, worried that he had scared the little girl. But Brennan just smiled back at him and spoke to the little girl.

"It's okay, Lyd. He's an old friend; he's a good man."

"Okay," Lydia said, accepting Brennan's vague explanation while finishing up the rest of her water. Brennan placed the glass in the sink before carrying Lydia back to the bedroom.

After about fifteen minutes, Brennan returned to the living room with a full laundry basket in her arms. She sat it down by the front door and walked back to the couch where Booth was once again sitting down. But this time he had grabbed the photo of Parker and the twins and was studying it closely. He looked up briefly when she walked into the room, and then again when she sat down next to him but soon returned his gaze to the photograph.

"That's Parker," he said softly. He turned to look at her again, and despite her limited people skills, she could see the question and emotion in his eyes.

"Where do you want me to start?"

"Well," he began, "You could begin by telling me who the four children are who seem to be living in your apartment. Who was the girl you you just carried in here? Why was she crying? What was going on back there?"

"That's Lydia. She had a nightmare and woke up screaming, and it scared Ellie so badly that she wet the bed..."

"So, who exactly is Lydia?" Booth hoped he didn't sound too pushy, but if he did, she either didn't notice, or didn't care.

"Liam is her little brother. They're my foster children."

"When did you get foster children?"

Brennan sighed and spoke softly as she began her story. "About a month ago. There was this FBI case, and I wasn't working it at first, but they specifically asked for my help, so I obliged. Their parents were brutally murdered for money while Liam cried in his crib and Lydia watched from a closet."

Booth watched a few stray tears ran down her face as she spoke. She hastily tried to wipe them away, but Booth wrapped and arm around her shoulder and pulled her close. He leaned in and kissed her on the cheek where a tear was slowly sliding down her face.

"I just couldn't let them be put in the system. No one would understand what Lydia had been through. She's only six, and I just... I don't know... I figured she could fit in with Ellie and Evie, and I couldn't separate her from Liam, so I found myself saying I'd take them." She rested her head on Booth's shoulder. "It was pretty impulsive of me, wasn't it?"

"No. Not at all. Not at all." He pulled her in for a real hug - a "guy hug" as he'd once dubbed them. He was so proud of his Bones. She'd come a long way since he first met her. In the first year of their partnership, she had sworn she never wanted children. But now here she was, loving and taking care of four children. God, he loved this woman more and more every moment of his life.

"I'm proud of you, Bones. You know that? You're an incredible woman."

Brennan pulled back and looked at Booth and smiled, then shook her head. "I just... followed my heart, like you would have told me to do. I seem to be doing that a lot lately, actually." She examined his face and saw pride and love reflected in his eyes, despite how tired they looked. But she knew there was another question that he wasn't voicing. She knew what it was, but she had no idea how to bring up the subject or break the news to him. Booth beat her to it.

"So, Ellie and Evie? They're the twins in this picture with Parker, right? Are... They're your biological daughters, aren't they?" he questioned, hoping that he didn't sound too upset or paranoid. Her biological clock had made her desire a child before, and her rational self had wanted his sperm to accomplish that. Had she gotten some other guy's stuff, or a whole other man? She was taking way too long to respond, and he noticed that she was twisting her mother's ring around on her finger. For once in his life, Booth couldn't read her, and he was becoming more and more anxious. Then she spoke a single word.

"Our." She said it so quietly that he almost didn't hear her.

"What? Our what, Bones?"

She turned to her and pursed her lips. "Our daughters, Booth. Ellie and Evie are _our_ biological daughters.

**A/N #2: I know, I know... everyone saw it coming, and some have complained about Booth and Brennan always having a daughter in fanfics, but I truly believe that Hart Hanson and company would give them a baby girl, too. Booth already has Parker, and it would just balance out their family if they had a girl. May not be realistic, but these ARE fictional characters, after all. I also believe that the name Christine (after Brennan's mom) would find its way into their daughter's name somehow. Either that, or it would be a completely unconventional name, but I couldn't write something like that. It took me months to get over the fact that Brennan's first name was Temperance. :-p**


End file.
